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- PDB-7t58: Crystal structure of Miz1 BTB domain -

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Basic information

Entry
Database: PDB / ID: 7t58
TitleCrystal structure of Miz1 BTB domain
ComponentsZinc finger and BTB domain-containing protein 17
KeywordsPROTEIN BINDING / Protein-protein interaction domain
Function / homology
Function and homology information


ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding ...ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding
Similarity search - Function
C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily ...C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger and BTB domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05333123838 Å
AuthorsLinhares, B.M. / Cierpicki, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Prediction of BTB domain ligandability guided by protein dynamics
Authors: Linhares, B.M. / Kharchenko, V. / Cierpicki, T. / Jaremko, L.
History
DepositionDec 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 17
B: Zinc finger and BTB domain-containing protein 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7384
Polymers25,5812
Non-polymers1562
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-20 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.919, 115.898, 64.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-379-

HOH

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Components

#1: Protein Zinc finger and BTB domain-containing protein 17 / Myc-interacting zinc finger protein 1 / Miz-1 / Zinc finger protein 151 / Zinc finger protein 60


Mass: 12790.745 Da / Num. of mol.: 2
Fragment: Protein-protein interaction domain (UNP residues 1-115)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB17, MIZ1, ZNF151, ZNF60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13105
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.053→41.305 Å / Num. obs: 13322 / % possible obs: 91.38 % / Redundancy: 6 % / Biso Wilson estimate: 28.2077185953 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.03
Reflection shellResolution: 2.053→2.127 Å / Rmerge(I) obs: 0.4381 / Num. unique obs: 1025

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Processing

Software
NameVersionClassification
REFMAC1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q81

2q81


Resolution: 2.05333123838→41.304806318 Å / SU ML: 0.234426987689 / Cross valid method: FREE R-VALUE / σ(F): 1.37849270882 / Phase error: 25.5241821045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231493196937 607 4.55637291698 %
Rwork0.182276851431 12715 -
obs0.184587497565 13322 91.4030874786 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.6214738525 Å2
Refinement stepCycle: LAST / Resolution: 2.05333123838→41.304806318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 8 216 1949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001957630716081771
X-RAY DIFFRACTIONf_angle_d0.4252405305292396
X-RAY DIFFRACTIONf_chiral_restr0.0377136785071284
X-RAY DIFFRACTIONf_plane_restr0.00264936705242306
X-RAY DIFFRACTIONf_dihedral_angle_d10.68940726891056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0534-2.260.3219451994411200.2333123223482646X-RAY DIFFRACTION77.3057574064
2.26-2.58690.2658180015241690.2125716873953243X-RAY DIFFRACTION94.8041122534
2.5869-3.25910.2562892440541490.1898246140433326X-RAY DIFFRACTION95.782800441
3.2591-41.3040.1938413846741690.1598342137373500X-RAY DIFFRACTION97.3467763332

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